2023年10月25日 · 1、Omit map"通过在密度map中排除特定区域的原子或分子，以突出该区域的密度变化。 具体来说，omit map 通常用于以下情况： 溶剂排除：将溶剂分子从密度地图中排除，以便更清晰地观察蛋白质或其他生物分子的位…

A composite omit map is an omit map covering the entire contents of the unit cell, generated by computing a number of omit maps covering specific regions, and combining the areas around the omitted regions. This allows a relatively bias-free map to be calculated for the structure without severely compromising phase quality.

There are two common types of electron density maps used by researchers, the 2Fo-Fc map and Fo-Fc map. The Fo-Fc map, known also as a difference or omit map, is used to show what has been overfit or not accounted for by the model, while the 2Fo-Fc map will include the Fo-Fc map and electron density around the model.

在文章审稿阶段，有时候审稿人要求展示密度图，包括2mFo-DFc map、Composite omit map，或者polder map。 2mFo-DFc map常使用1σ的contour level，而对于difference map一般使用较高的contour level，例如Composite omit map可以使用2σ。

This guide demonstrates how to calculate a F o − F c omit map using Servalcat. A F o − F c omit map is a difference map calculated after removing (omitting) certain atoms from the model. This is useful for visualising the presence of ligands or other features not explicitly included in the model.

For isomorphous difference maps (Fobs-Fobs), use phenix.fobs_minus_fobs_map (documentation to be added). For omit maps, including composite omit maps and iterative build omit maps, use the AutoBuild wizard.

2024年12月3日 · 要选pdb作模拟的初始结构或者是experimental reference for model validation的话可以先用这方法检查一下。这只是个快速测一下的方法，正式算文献中的omit map会用更专门的工具(phenix选单可以找到正式omit map的工具)

2024年4月9日 · 经常看到明明衍 射超好的数据，可是却被一个不知道谁教的死板指令 “omit -3 50” 活 生生的砍在了一个固定的分辨率。 细究起来，你会发现，很多学生根本不知道这个指令是啥意思，只知道说： 这样可以提高完整度，降低R1值。

‘comit’ Calculates composite omit maps by omitting spheres of density from the assymetric unit and reconsructing those spheres using sigma-a weighted maps. ‘comit’ can use one of two methods. A fast calculation using the output from refmac can generate a very good approximation to the full composite omit map with the correct choice of ...

Sigma-A weighted composite omit map (at 1.25 sigma) calculated using the MR model. The true structure is shown in brown, the MR model in green. Model bias is reduced around the MR coordinates.